This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 6 Casal2 model configurations (3 BetaDiff and 3 ADOL-C).
The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-6 vs. 2e-3).
The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-6 vs. 2e-3).
The main characteristics of the Test Case HAK (hake) CASAL model are:
Observation data include:
Parameters estimated include:
The CASAL MCMC options include
The Casal2 ADOL-C and BetaDiff MCMC options include
## [1] "Thu Jan 13 13:42:17 2022"
## R version 4.1.2 (2021-11-01)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux bookworm/sid
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## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
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## other attached packages:
## [1] Casal2_21.11 casal_2.30 devtools_2.4.3 usethis_2.1.5 rlist_0.4.6.2
## [6] ggthemes_4.2.4 gridExtra_2.3 coda_0.19-4 ggmcmc_1.5.1.1 ggplot2_3.3.5
## [11] tidyr_1.1.4 huxtable_5.4.0 dplyr_1.0.7 plyr_1.8.6
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## [1] Rcpp_1.0.7 lattice_0.20-45 prettyunits_1.1.1 ps_1.6.0
## [5] assertthat_0.2.1 rprojroot_2.0.2 digest_0.6.29 utf8_1.2.2
## [9] R6_2.5.1 evaluate_0.14 pillar_1.6.4 rlang_0.4.12
## [13] data.table_1.14.2 callr_3.7.0 jquerylib_0.1.4 rmarkdown_2.11
## [17] desc_1.4.0 stringr_1.4.0 munsell_0.5.0 compiler_4.1.2
## [21] xfun_0.29 pkgconfig_2.0.3 pkgbuild_1.3.1 htmltools_0.5.2
## [25] tidyselect_1.1.1 tibble_3.1.6 reshape_0.8.8 fansi_0.5.0
## [29] crayon_1.4.2 withr_2.4.3 grid_4.1.2 jsonlite_1.7.2
## [33] GGally_2.1.2 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2
## [37] magrittr_2.0.1 scales_1.1.1 cli_3.1.0 stringi_1.7.6
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## [45] bslib_0.3.1 ellipsis_0.3.2 generics_0.1.1 vctrs_0.3.8
## [49] RColorBrewer_1.1-2 tools_4.1.2 glue_1.6.0 purrr_0.3.4
## [53] processx_3.5.2 pkgload_1.2.4 fastmap_1.1.0 yaml_2.2.1
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# source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_CASAL_MCMC_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MCMC_files.R')
For the diagnostics below, the last 10000 samples for each chain are used and subsampled at 10, so that 1000 samples are input into the diagnostic functions.